Genetic Variant SLC14A1:c.-22+2360C>A (chr18-45727373-C-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001128588.4(SLC14A1):c.102C>A(p.Gly34Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 1,550,130 control chromosomes in the GnomAD database, including 177,838 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.41 ( 14105 hom., cov: 33)

Exomes 𝑓: 0.48 ( 163733 hom. )

Consequence

SLC14A1
NM_001128588.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.06

Variant links:

Genes affected

SLC14A1 (HGNC:10918): (solute carrier family 14 member 1 (Kidd blood group)) The protein encoded by this gene is a membrane transporter that mediates urea transport in erythrocytes. This gene forms the basis for the Kidd blood group system. [provided by RefSeq, Mar 2009]

SLC14A1 links:

ENSG00000288545 (HGNC:):

ENSG00000288545 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 18-45727373-C-A is Benign according to our data. Variant chr18-45727373-C-A is described in ClinVar as [Benign]. Clinvar id is 3059256.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7 link	c.-22+2360C>A		intron_variant	Intron 2 of 9	ENST00000321925.9	NP_056949.4	Q13336-1G0W2N5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9 link	c.-22+2360C>A		intron_variant	Intron 2 of 9	1	NM_015865.7	ENSP00000318546.4		Q13336-1

Frequencies

GnomAD3 genomes

AF:

0.415

AC:

63095

AN:

152014

Hom.:

14107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.234

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.476

Gnomad ASJ

AF:

0.422

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.486

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.441

GnomAD3 exomes

AF:

0.472

AC:

72517

AN:

153612

Hom.:

17494

AF XY:

0.470

AC XY:

38287

AN XY:

81508

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.511

Gnomad ASJ exome

AF:

0.427

Gnomad EAS exome

AF:

0.538

Gnomad SAS exome

AF:

0.426

Gnomad FIN exome

AF:

0.494

Gnomad NFE exome

AF:

0.494

Gnomad OTH exome

AF:

0.478

GnomAD4 exome

AF:

0.481

AC:

672907

AN:

1397998

Hom.:

163733

Cov.:

AF XY:

0.480

AC XY:

330635

AN XY:

689316

show subpopulations

Gnomad4 AFR exome

AF:

0.228

Gnomad4 AMR exome

AF:

0.512

Gnomad4 ASJ exome

AF:

0.425

Gnomad4 EAS exome

AF:

0.542

Gnomad4 SAS exome

AF:

0.430

Gnomad4 FIN exome

AF:

0.497

Gnomad4 NFE exome

AF:

0.492

Gnomad4 OTH exome

AF:

0.462

GnomAD4 genome

AF:

0.415

AC:

63104

AN:

152132

Hom.:

14105

Cov.:

AF XY:

0.414

AC XY:

30756

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.234

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.422

Gnomad4 EAS

AF:

0.517

Gnomad4 SAS

AF:

0.413

Gnomad4 FIN

AF:

0.486

Gnomad4 NFE

AF:

0.492

Gnomad4 OTH

AF:

0.440

Alfa

AF:

0.453

Hom.:

7941

Bravo

AF:

0.408

Asia WGS

AF:

0.430

AC:

1500

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC14A1-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over